Contacts of the helix formed by residues 402 - 406 (chain A) in PDB entry 2F4J
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 402 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A ARG 5.8 2.5 - - - +
363A ASP* 4.1 13.5 - - - +
367A ARG* 3.4 30.3 - - - +
384A LEU* 6.3 2.2 - - + -
400A LYS 4.7 0.7 - - - +
401A PHE* 1.4 84.9 - - + +
403A ILE* 1.3 63.4 - - - +
404A LYS 3.3 2.7 - - - -
405A TRP* 3.0 27.4 + - + -
406A THR* 2.7 20.8 + - - +
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Residues in contact with ILE 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A PHE* 2.8 23.8 + - + +
402A PRO* 1.3 69.0 - - - +
404A LYS* 1.3 62.2 + - - +
406A THR* 3.2 18.7 + - - +
411A LEU* 3.3 34.8 - - + +
445A LEU* 3.9 45.1 - - + +
448A VAL* 4.1 23.6 - - + +
449A TYR* 5.6 0.9 - - + +
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Residues in contact with LYS 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A PRO 3.1 1.6 + - - -
403A ILE* 1.3 75.7 - - - +
405A TRP* 1.3 80.1 + - + +
406A THR 3.5 0.4 - - - +
423A TRP* 4.8 1.9 + - - -
427A VAL* 3.5 14.4 - - - +
438A SER* 4.1 16.4 - - - -
439A PRO* 3.0 46.9 + - + +
440A TYR* 3.5 41.9 + - + -
443A ILE 5.1 5.3 + - - -
445A LEU* 3.7 29.4 - - + -
448A VAL* 5.1 3.6 - - + -
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Residues in contact with TRP 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A LEU* 6.2 2.5 - - + -
363A ASP* 6.2 0.4 - - - +
364A LEU 3.5 26.0 - - - +
365A ALA* 3.6 10.4 - - + +
367A ARG* 3.5 27.4 - - + +
402A PRO* 3.0 25.0 + - + +
404A LYS* 1.3 100.4 - - + +
406A THR* 1.3 62.1 + - - +
407A ALA 3.8 0.7 + - - -
420A SER 4.9 0.7 - - - +
423A TRP* 3.7 6.1 - - - -
424A ALA* 3.6 28.6 - - + +
427A VAL* 3.4 28.8 - - + +
428A LEU 4.7 0.2 - - - -
431A GLU* 2.9 39.4 + - - -
438A SER* 6.1 0.4 - - - -
439A PRO* 3.7 24.7 - - + -
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Residues in contact with THR 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A PHE* 3.6 21.9 - - + +
402A PRO* 2.7 27.5 + - - +
403A ILE 3.2 4.8 + - - +
404A LYS 5.2 0.2 - - - -
405A TRP* 1.3 79.3 - - - +
407A ALA* 1.3 69.3 + - - +
408A PRO* 3.7 1.0 - - - +
410A SER* 3.4 27.1 - - - -
411A LEU* 3.5 38.5 - - + +
416A PHE* 4.6 5.7 - - + -
423A TRP* 3.9 8.9 + - - -
452A LEU* 5.0 3.1 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il